Re: [AMBER] error in measuring distances in amber 11

From: Thomas Cheatham <>
Date: Mon, 19 Dec 2011 09:16:37 -0700 (Mountain Standard Time)

Please do not repost the same message to the list repeatedly...

> I tried to measure the distance using ptraj of amber 11 using the
> command: distance
> dist_73-84_139-150 :73.CA-84.CA :139.CA-150@CA out distance.dat and I
> got output file with the measured distance with all distances equal zero.

As pointed out, the syntax you used is incorrect. It should be
  :73-84.CA :139-150.CA

Also, take a look at the output from ptraj. Normally this is best piped
to a file:

ptraj prmtop >& ptraj.out

For each distance, information on the atom selection ptraj found will be
printed. Likely, as the mask was misspecified, all atoms were selected
and ptraj calculated the center of mass of all atoms to the center of mass
of all atoms which would give zero distance.

If ptraj in amber8 and amber11 are different, likely they are interpreting
the incorrect atom mask specification differently. Look at the respective
outputs. If not enough information is present, increase the verbosity.

prnlev 3


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Received on Mon Dec 19 2011 - 08:30:08 PST
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